https://github.com/vhchavez/moly
Molecular Visualization powered by Plotly
https://github.com/vhchavez/moly
jupyter molecular-structures plotly
Last synced: 10 months ago
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Molecular Visualization powered by Plotly
- Host: GitHub
- URL: https://github.com/vhchavez/moly
- Owner: VHchavez
- License: bsd-3-clause
- Created: 2020-02-12T13:58:40.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2022-08-28T16:00:33.000Z (almost 4 years ago)
- Last Synced: 2025-07-06T08:42:35.900Z (11 months ago)
- Topics: jupyter, molecular-structures, plotly
- Language: Python
- Homepage:
- Size: 1.59 MB
- Stars: 17
- Watchers: 1
- Forks: 4
- Open Issues: 10
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION.cff
Awesome Lists containing this project
README
***
Try it now:
### Features:
Geometry
Volumes from Cube Files
### Supports:
xyz files
Psi4 geometries
QCElemental molecules
### Installation
* git:
```
git clone https://github.com/VHchavez/moly.git
cd moly
pip install .
```
* pip:
```
pip install moly
```
* conda:
```
coming soon!
```
* ### Basic Geometry
*Define a figure and add molecules to it.*
```
import moly
fig = moly.Figure()
molecule = moly.Molecule.from_file("caffeine.xyz")
fig.add_molecule("caffeine", molecule)
fig.show()
```
* ### Basic Layering
*Geometries can be brought from different sources and be thrown in the same figure*
```
#Molecules from QCArchive
import qcportal as ptl
client = ptl.FractalClient()
#Get molecule from QCArchive
ds = client.get_collection("ReactionDataset", "S22")
dimers = ds.get_molecules()
ammonia_dimer = dimers.loc['Ammonia Dimer', 'molecule'][0]
#Different surfaces are available.
#Resolution can be increased if saving figure is desired.
fig = moly.Figure(figsize=(800,800), surface="shiny")
fig.add_molecule("dimer", ammonia_dimer)
fig.add_molecule("bucky ball", moly.Molecue.from_file("bucky.xyz"))
fig.show()
```
#### Copyright
Copyright (c) 2020, VH Chavez
##### Acknowledgements
Project based on the
[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.1.
Victor H. Chavez was supported by a fellowship from The Molecular Sciences Software Institute under NSF grant OAC-1547580.